RetrogeneDB ID: retro_mmus_76

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:20665333..20666653(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000047565
• Aliases: Acot10, Acate3, MT-ACT48, p48
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Acot9
• Ensembl ID: ENSMUSG00000025287
• Aliases: Acot9, 0610041P13Rik, Acate2, C76421, MT-ACT48, U8, p48
• Description: acyl-CoA thioesterase 9 [Source:MGI Symbol;Acc:MGI:1928939]

Sequence

>retro_mmus_76
ATGAAGCGGGCAGCGATGAGGCTTTGGACCTTGAACAAGGGGCTTCTTACTCATGGCAGAGGACTATCTCAAGGATCCCA
ATACAAAATAAGTGAACCCTTACACATCCATCAAGTTCAAGTCAAGCTGCGGGAGATAGTAGGTATTTCCACAGTCTGGA
GAGACCATGTACAAGCAATGGAGGAAAGGAAGTTACTTCATAGTTTTTTGCCTAAATCACAGAAAGTCCTACCACCGAGG
AAAATAAGGGATAGTTACATTGAAGTTCTCCTACCTTTGGGTACTGACCCTGAACTACGAGACAAATATGTGACTGTTCA
AAATACAGTAAGATTTGGCAGGATTCTTGAGGACCTTGACAGCTTAGGAGTTCTTGTTTGCTACATGCACAACCACAATC
ATTCTACCAATATGTCTCTTTTATCAATAGTTACAGTCCTGGTGGACAAGATTGATATGTGTAAACACAGCTTAAGCCCT
GAACAGGACATTAAGTTCACTGGCCATGTTAGCTGGGTTGGAAATACAACCATGGAAGTGAAGATGAAAATGTTCCAGCT
GCACGATGATGAGACATATTGGCCTGTTTTGGATGCAACCTTTGTAATGGTGGCTCAAGATTCTGAAAATAAGAGGCCGG
CATTTGTAAATCCACTCATTCCGGAAAATAAAGAAGAAGAAGAGCTCTTTACACAAGGAGAATTGAACAAGAGCCGAAGG
ATTGCCTTTAGCACCAGTTCATTACTGAAAGTGGCTCCCAGTTCTGAGGAGAGGAATATCATACATGAACTGTTTCTTAG
CACACTGGATCCAAAGACTATAAGTTTTCAGAGTCGAATTTTGCCTCCTAAGGCAGTGTGGATGGAGGATACAAAACTCA
AGAGCTTGGATATTTGTCACCCTCAGGAACGAAATGTATTCAATCGGATCTTTGGTGGTTTTCTTATGAGAAAAGCATAT
GAACTTGCATGGGCTACTGCTTGTAGCTTTGGAGGTTCTCGGCCATATGTGGTAACAGTAGATGATATCATGTTTCAGAA
GCCTGTTGAAGTTGGTTCATTGCTCTTTCTTTCTTCACAGGTATGCTTCACCCAGGGTAATTACATTCAAGTCAGAGTCC
ATAGTGAAGTGTTCTCTCTTGACAGTCGTGAGCATATGACCACCAATGTCTTTCATTTTACATTCATGTCAGAAAAAGAA
GTACCCTTGATTTTCCCTAAAACATATGGAGAGTCCATGTTGTATTTAGATGGACAGCGACATTTCAAGTCTATGAGTAC
CCCAGTAACCTTAAAAAAGGACTACCCTGTGGAACCCTAG

Alignment

ORF - retro_mmus_76 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKRAAIRLWTLNKGLLTHGRGLSQGSQYKISEPLHIHQVRDKLREIVGVSTVWRDHVKAMEERKLLHSFL
          MKRAA.RLWTLNKGLLTHGRGLSQGSQYKISEPLHIHQV..KLREIVG.STVWRDHV.AMEERKLLHSFL
Retrocopy MKRAAMRLWTLNKGLLTHGRGLSQGSQYKISEPLHIHQVQVKLREIVGISTVWRDHVQAMEERKLLHSFL

Parental  PKSQKVLPPRKMRDSYIEVLLPLGTDPELRDKYVTVQNTVRFGRILEDLDSLGVLVCYMHNHNHSTKMSP
          PKSQKVLPPRK.RDSYIEVLLPLGTDPELRDKYVTVQNTVRFGRILEDLDSLGVLVCYMHNHNHST.MS.
Retrocopy PKSQKVLPPRKIRDSYIEVLLPLGTDPELRDKYVTVQNTVRFGRILEDLDSLGVLVCYMHNHNHSTNMSL

Parental  LSIVTVLVDKIDMCKHSLSPEQDIKFTGHVSWVGNTSMEVKMKMFQLHNDEKYWPVLDATFVMVARDSEN
          LSIVTVLVDKIDMCKHSLSPEQDIKFTGHVSWVGNT.MEVKMKMFQLH.DE.YWPVLDATFVMVA.DSEN
Retrocopy LSIVTVLVDKIDMCKHSLSPEQDIKFTGHVSWVGNTTMEVKMKMFQLHDDETYWPVLDATFVMVAQDSEN

Parental  KGPAFVNPLIPENKEEEELFKQGELNKSRRIAFSTSSLLKVAPSSEERNIIHELFLTTLDPKTISFQSRI
          K.PAFVNPLIPENKEEEELF.QGELNKSRRIAFSTSSLLKVAPSSEERNIIHELFL.TLDPKTISFQSRI
Retrocopy KRPAFVNPLIPENKEEEELFTQGELNKSRRIAFSTSSLLKVAPSSEERNIIHELFLSTLDPKTISFQSRI

Parental  LPPKAVWMEDTKLKSLDICHPQERNVFNRIFGGFLMRKAYELAWATACSFGGSRPYVVTVDDIMFQKPVE
          LPPKAVWMEDTKLKSLDICHPQERNVFNRIFGGFLMRKAYELAWATACSFGGSRPYVVTVDDIMFQKPVE
Retrocopy LPPKAVWMEDTKLKSLDICHPQERNVFNRIFGGFLMRKAYELAWATACSFGGSRPYVVTVDDIMFQKPVE

Parental  VGSLLFLSSQVCFTQDNYIQVRVHSEVSSLDSREHMTTNVFHFTFMSEKEVPLIFPKTYGESMLYLDGQR
          VGSLLFLSSQVCFTQ.NYIQVRVHSEV.SLDSREHMTTNVFHFTFMSEKEVPLIFPKTYGESMLYLDGQR
Retrocopy VGSLLFLSSQVCFTQGNYIQVRVHSEVFSLDSREHMTTNVFHFTFMSEKEVPLIFPKTYGESMLYLDGQR

Parental  HFKSMSTPVTLKKDYPVEP
          HFKSMSTPVTLKKDYPVEP
Retrocopy HFKSMSTPVTLKKDYPVEP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.19 RPM	13.15 RPM
SRP007412_cerebellum	0.04 RPM	6.99 RPM
SRP007412_heart	0.00 RPM	12.67 RPM
SRP007412_kidney	0.06 RPM	22.93 RPM
SRP007412_liver	0.00 RPM	2.65 RPM
SRP007412_testis	13.58 RPM	27.99 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_76 was not detected

EST

No EST(s) were mapped for retro_mmus_76 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_39302	861 libraries	197 libraries	11 libraries	1 library	2 libraries

The graphical summary, for retro_mmus_76 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_76 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_76 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000007768	1 retrocopy	retro_mdom_332,
Mus musculus	ENSMUSG00000025287	1 retrocopy	retro_mmus_76 ,
Otolemur garnettii	ENSOGAG00000002305	1 retrocopy	retro_ogar_954,